[2024-01-24 13:40:35,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference
[2024-01-24 13:40:36,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,538] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg42f6610c-745f-4817-81c2-efd1b0964d56/GCF_022568775.1_ASM2256877v1_genomic.fna.gz | prodigal -d GCF_022568775.1_ASM2256877v1_genomic.fna/cds.fna -a GCF_022568775.1_ASM2256877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,679] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,680] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,680] [INFO] Running command: hmmsearch --tblout GCF_022568775.1_ASM2256877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/reference_markers.hmm GCF_022568775.1_ASM2256877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,982] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,011] [INFO] Query marker FASTA was written to GCF_022568775.1_ASM2256877v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,011] [INFO] Task started: Blastn
[2024-01-24 13:40:46,011] [INFO] Running command: blastn -query GCF_022568775.1_ASM2256877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/reference_markers.fasta -out GCF_022568775.1_ASM2256877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,038] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:47,039] [INFO] Target genome list was writen to GCF_022568775.1_ASM2256877v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,047] [INFO] Task started: fastANI
[2024-01-24 13:40:47,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f6610c-745f-4817-81c2-efd1b0964d56/GCF_022568775.1_ASM2256877v1_genomic.fna.gz --refList GCF_022568775.1_ASM2256877v1_genomic.fna/target_genomes.txt --output GCF_022568775.1_ASM2256877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:02,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:02,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:02,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:02,266] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:02,266] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:02,266] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	79.187	338	1010	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.1111	366	1010	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	79.0592	313	1010	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.9564	371	1010	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.9547	324	1010	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	78.8549	369	1010	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.8361	352	1010	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	78.8119	350	1010	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.7712	320	1010	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.6826	384	1010	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.6203	327	1010	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.5505	305	1010	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.4349	335	1010	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.9714	300	1010	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.9111	222	1010	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	77.8396	209	1010	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	77.7622	214	1010	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.6967	243	1010	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	77.6874	221	1010	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.6599	206	1010	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	77.604	303	1010	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	77.4167	203	1010	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	77.0729	157	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:02,268] [INFO] DFAST Taxonomy check result was written to GCF_022568775.1_ASM2256877v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:02,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:02,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:02,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/checkm_data
[2024-01-24 13:41:02,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:02,302] [INFO] Task started: CheckM
[2024-01-24 13:41:02,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022568775.1_ASM2256877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022568775.1_ASM2256877v1_genomic.fna/checkm_input GCF_022568775.1_ASM2256877v1_genomic.fna/checkm_result
[2024-01-24 13:41:33,166] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:33,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,187] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:33,188] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:33,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022568775.1_ASM2256877v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:33,189] [INFO] Task started: Blastn
[2024-01-24 13:41:33,189] [INFO] Running command: blastn -query GCF_022568775.1_ASM2256877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c6a97cf-0be4-4a8e-99c2-0834205415b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_022568775.1_ASM2256877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,145] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:35,146] [INFO] Target genome list was writen to GCF_022568775.1_ASM2256877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:35,175] [INFO] Task started: fastANI
[2024-01-24 13:41:35,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f6610c-745f-4817-81c2-efd1b0964d56/GCF_022568775.1_ASM2256877v1_genomic.fna.gz --refList GCF_022568775.1_ASM2256877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022568775.1_ASM2256877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,814] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,815] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014873475.1	s__Sphingomicrobium sp014873475	81.2344	625	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489495.1	s__Sphingomicrobium daechungense	81.1402	585	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489515.1	s__Sphingomicrobium sediminicola	81.0574	557	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	79.2676	269	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	79.2253	440	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620665.1	s__Sphingomicrobium sp000620665	79.2014	415	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	79.1729	339	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.0098	298	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	78.8571	313	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	78.854	350	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	78.8088	351	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812825.1	s__Sphingomicrobium sp013812825	78.6968	352	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.6932	383	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.5965	329	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.5504	305	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812805.1	s__Sphingomicrobium sp013812805	78.3747	253	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806275.1	s__Sphingomicrobium sp902806275	78.3283	233	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859635.1	s__Sphingomonas panacisoli	77.8711	207	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197685.1	s__Sphingomonas dokdonensis	77.7781	213	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806295.1	s__Sphingomicrobium sp902806295	77.4964	179	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	77.3928	160	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	77.0729	157	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,816] [INFO] GTDB search result was written to GCF_022568775.1_ASM2256877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,824] [INFO] DFAST_QC result json was written to GCF_022568775.1_ASM2256877v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,824] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,825] [INFO] Total running time: 0h1m12s